HHsearch alignment for GI: 254780345 and conserved domain: cd00447
>cd00447 NusB_Sun RNA binding domain of NusB (N protein-Utilization Substance B) and Sun (also known as RrmB or Fmu) proteins. This family includes two orthologous groups exemplified by the transcription termination factor NusB and the N-terminal domain of the rRNA-specific 5-methylcytidine transferase (m5C-methyltransferase) Sun. The NusB protein plays a key role in the regulation of ribosomal RNA biosynthesis in eubacteria by modulating the efficiency of transcriptional antitermination. NusB along with other Nus factors (NusA, NusE/S10 and NusG) forms the core complex with the boxA element of the nut site of the rRNA operons. These interactions help RNA polymerase to counteract polarity during transcription of rRNA operons and allow stable antitermination. The transcription antitermination system can be appropriated by some bacteriophages such as lambda, which use the system to switch between the lysogenic and lytic modes of phage propagation. The m5C-methyltransferase Sun shares the
Probab=99.97 E-value=3.7e-29 Score=195.38 Aligned_cols=126 Identities=33% Similarity=0.425 Sum_probs=117.3
Q ss_pred HHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHH
Q ss_conf 99999999999995699989999999985310013221120144343999999999999989999999997410357633
Q gi|254780345|r 19 ARLAAVQALYQIDIIGCSTTEIISEYETYRFCADTELDVESVYLHVDLEWFRVIIHGVMDRKQHIDLLISSCLTEKWSFS 98 (170)
Q Consensus 19 aR~~aiq~Ly~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~d~~~~~~lv~~v~~~~~~id~~I~~~l~~~w~~~ 98 (170)
T Consensus 2 AR~~a~~~L~~~~~~~~~~~~~l~~~~~-----------~~~l~~~d~~~~~~lv~gv~~~~~~ld~~i~~~l-~~~~~~ 69 (129)
T cd00447 2 AREIAFQALYQVEIRNGISLEAVLSALE-----------KLQLAKKDRPFALELVYGVLRNLPELDDIISPLL-KKWLLD 69 (129)
T ss_pred HHHHHHHHHHHHHHHCCCHHHHHHHHHH-----------HCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-CCCCHH
T ss_conf 8999999999998209999999999998-----------7789778999999999999996999999999982-788031
Q ss_pred HCCCHHHHHHHHHHHHHHHCC-CCCCCCHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHH
Q ss_conf 235348999999999986435-5781033988999999833877231499999999952
Q gi|254780345|r 99 RLDMILCSILRAGVLELIECH-SVPVEVIISEYVCIAHDFFYGDEPKFINAVLDKVSRK 156 (170)
Q Consensus 99 rl~~~~~~iLr~a~~El~~~~-~~p~~vvInE~V~lak~f~~~~~~~fVNaVL~ki~k~ 156 (170)
T Consensus 70 ~~~~i~~~iLrl~~~el~~~~~~ip~~~~InE~v~lak~~~~~~~~~fvNavLr~i~r~ 128 (129)
T cd00447 70 RLDKVDRAILRLLLYELYQLLYDVPPPVAINEAVELAKRFGDDDSAKFVNGVLRRIAKE 128 (129)
T ss_pred HHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHCC
T ss_conf 10088899999999999985058985167899999999867886320079997798734